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Forum: Bioinformatics 05-10-2017, 09:12 PM
Replies: 3
Views: 1,595
Posted By jorvis
I realize that those two reads didn't actually...

I realize that those two reads didn't actually align, so the SAM lines were pretty minimal. Here are a pair which did:

SN7001163:162:C4A1UACXX:1:1101:1174:2116 81 ...
Forum: Bioinformatics 05-10-2017, 09:03 PM
Replies: 3
Views: 1,595
Posted By jorvis
Read direction lost with BWA in SAM output?

I've tried two different header styles in my input FASTQ headers when running BWA:

@SN7001163:162:C4A1UACXX:1:1101:1062:2076/1

and

@SN7001163:162:C4A1UACXX:1:1101:1062:2076 1:N:0:GTCCGCA
...
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